#!/bin/bash -e

# general
LUMPY_HOME=~/lumpy-sv

# HEXDUMP is used to determine if a file is a CRAM
HEXDUMP=`which hexdump || true`

LUMPY=`which lumpy || true`
SAMBLASTER=`which samblaster || true`
# either sambamba or samtools is required
SAMBAMBA=`which sambamba || true`
SAMTOOLS=`which samtools || true`

# python 2.7 or newer, must have pysam, numpy installed
PYTHON=`which python || true`

# python scripts
PAIREND_DISTRO=$LUMPY_HOME/scripts/pairend_distro.py
BAMGROUPREADS=$LUMPY_HOME/scripts/bamkit/bamgroupreads.py
BAMFILTERRG=$LUMPY_HOME/scripts/bamkit/bamfilterrg.py
BAMLIBS=$LUMPY_HOME/scripts/bamkit/bamlibs.py
